I have had excellent luck running quarries using the following setup:
Use ShadwDrgn's automatic water mills setup to generate at least 34 EU/tick (17 water mills).
Connect that to an MFE using tin cables.
Connect the MFE to an LV transformer using no more than two double-insulated gold cables.
Connec the LV transformer to an Energy Link using no more than five insulated copper cables.
Your quarry should now run pretty fast and be able to tolerate bucket placement problems in the water mills thanks to the MFE.
Re: Crashing instantly upon joining a server
Have you tried renaming your existing Technic installation and re-running the launcher?
To do so, click on the Start Menu, go to Run..., and put in:
%appdata%
Look for the ".techniclauncher" folder and rename it to something else (so the launcher doesn't see it).
Re-run the launcher. It will download the pack from scratch. Now try connecting to a server.
Note that your single-player world save is still in that renamed folder, so you will want to move it to the new installation when you're done.
What kind of beeping does your server do? Unless you have installed a specific server-side mod that makes your server beep when a client logs in, it shouldn't do that.
Have you considered running the Tekkit server in a Linux virtual machine? You have enough resources for it, and it would eliminate some potential causes (such as your anti-virus software).
We're using McMMO and Wormhole X-treme on ours, and it works out pretty well. The only complaint I have is that McMMO doesn't recognize the new tools and ores for skills.
Please don't feel too stupid when you read this, but the recipe calls or Iron Ingots instead of Tin Ingots. If it helps, I accidentally tried making a Battery Box in my Alloy Furnace last night.
The first thing you want to do, and it sounds like you already know this, is to install Oracle Java 7 onto your Ubuntu system. You should follow these instructions for getting it setup.
Once that is installed, download the Tekkit server files, extract them to a directory of your choosing, and run it with the command inside of the launch.bat file.
Did you follow the video in this thread exactly? It sounds like you might have one of the RedPower machines facing the wrong direction.
These setups work fine on our server, so it's not a problem with Tekkit (unless, of course, you have modified the base installation).